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Nitsche, A.

Publications and source records attributed to Nitsche, A..

15 recordsLinked to original sources
bioRxiv2024

First report of pathogenic Leptospira in Sri Lankan bats: A potential reservoir risk

BackgroundLeptospirosis is a bacterial infection caused by spirochetes of the genus Leptospira. It affects both humans and animals, posing a significant public health threat worldwide. In Sri Lanka, leptospirosis causes annual outbreaks, particularly during the monsoon seasons. The disease is often difficult to diagnose and can have a high mortality rate. Bats are potential reservoirs for Leptospira in other countries. This study investigated the presence and diversity of Leptospira in bats inhabiting the Wavulgalge, a natural cave in Sri Lanka. Methodology/Principal FindingsUsing PCR and Sanger sequencing techniques, Leptospira borgpetersenii and Leptospira kirschneri were identified in Miniopterus fuliginosus and Rousettus leschenaultii bats. Out of 148 bat urine samples, 16 tested positive via RT-qPCR, with M. fuliginosus samples harboring L. borgpetersenii and one R. leschenaultii sample harboring L. kirschneri revealed by Sanger sequencing method. Conclusions/SignificanceThese findings enhance the understanding of the zoonotic role of Sri Lankan bats in Leptospira transmission. Author SummaryLeptospirosis is a bacterial disease that affects both humans and animals, particularly in tropical regions. It spreads through contact with water or soil contaminated by the urine of infected animals. In Sri Lanka, leptospirosis poses a significant public health challenge, with frequent outbreaks during the rainy season. However, while much research has focused on domestic animals as potential carriers, the role of bats in the transmission of this disease has not been fully explored. In this study, we investigated whether bats in Sri Lanka can act as carriers of Leptospira bacteria, which could contribute to the spread of leptospirosis to humans. We focused on a population of bats from the Wavulgalge cave and tested them for the presence of Leptospira using molecular methods. Our results provide the first evidence that Leptospira is present in Sri Lankan bats, highlighting their potential role as a reservoir for the bacteria. These findings are important because they suggest that bats, like rodents and livestock, could contribute to the spread of leptospirosis in Sri Lanka. Understanding which animals carry the bacteria helps inform public health strategies, allowing for more targeted surveillance and control measures. By including bats in these efforts, we can better prevent future outbreaks of leptospirosis and protect at-risk communities. This study also contributes to the broader understanding of how wildlife can influence human health, especially in tropical environments where human-animal interactions are common. Our work emphasizes the need for a One Health approach, which considers the connections between human, animal, and environmental health, to tackle neglected diseases like leptospirosis.

microbiology↗
bioRxiv2024

Aging and viral evolution impair immunity against dominant pan-coronavirus-reactive T cell epitope

Immune evasion by escape mutations subverts immunity against SARS-CoV-2. A role of pan-coronavirus immunity for more durable protection is being discussed but has remained understudied. We here investigated the effects of age, mutations, and homo-/heterologous vaccination regimens on the dominant pan-coronavirus-specific cellular and humoral epitope iCope after SARS-CoV-2 infection and vaccination in detail. In the older, quantitatively, and qualitatively reduced iCope-reactive CD4+ T cell responses with narrow TCR repertoires could not be enhanced by vaccination and were further compromised by emerging spike mutations. In contrast pan-coronavirus-reactive humoral immunity was affected only by mutations and not by age. Our results reveal a distinct deficiency of the dichotomous layer of pan-coronavirus immunity in the older, critical for long-term protection against SARS-CoV-2 variants. One-Sentence SummaryAging and viral evolution impair dominant pan-coronavirus immunity, a hallmark of efficient and broad immune competence against SARS-CoV-2

immunology↗
bioRxiv2024

First Report of Nipah virus shed in urine by fruit bats (Pteropus medius), Sri Lanka

Nipah virus is an emerging pathogen with high public health relevance, causing outbreaks in South- and Southeast Asia with high case fatality rates. The natural reservoir host are fruit bats (Pteropus spp). In this study, we confirmed the presence of Nipah virus for the first time in Sri Lanka and are proving the genetic relatedness to Nipah virus strains from southern India, causing outbreaks in 2007, 2018, 2019 and 2023. It is noteworthy that the shedding of the Nipah Virus may have a temporal variation that correlates with the breeding season of Pteropus medius. Furthermore, preventive measures and possible mechanisms influencing viral shedding are discussed.

microbiology↗
bioRxiv2023

MpoxRadar: a worldwide Mpox genomic surveillance dashboard

Monkeypox (Mpox) is mutating at an exceptional rate for a DNA virus and its global spread is concerning, making genomic surveillance a necessity. With MpoxRadar, we provide an interactive dashboard to track virus variants on mutation level worldwide. MpoxRadar allows users to select among different genomes as reference for comparison. The occurrence of mutation profiles based on the selected reference is indicated on an interactive world map that shows the respective geographic sampling site in customizable time ranges to easily follow the frequency or trend of defined mutations. Furthermore, the user can filter for specific mutations, genes, countries, genome types, and sequencing protocols and download the filtered data directly from MpoxRadar. On the server, we automatically download all Mpox genomes and metadata from the National Center for Biotechnology Information (NCBI) on a daily basis, align them with the different reference genomes, generate mutation profiles, which are stored and linked to the available metainformation in a database. This makes MpoxRadar a practical tool for the genomic survaillance of Mpox, supporting users with limited computational resources. MpoxRadar is open-source and freely accessible at https://MpoxRadar.net. GRAPHICAL ABSTRACT O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

bioinformatics↗
bioRxiv2022

Possible adaption of the 2022 Monkeypox virus to the human host through gene duplication and loss

Poxviruses are known to evolve slower than RNA viruses, with rearrangements such as gene gain and loss as the main driver for host adaption. In 2022 the world is being challenged by the largest global outbreak so far of Monkeypox virus, and the virus seems to have established itself in the human community. Here we report five MPXV genomes with extensive gene duplication and loss, including duplications of up to 18,000 bp to the opposed genome end, and deletions at the site of insertion of up to 16,000 bp, as a possible adaption to the human host.

molecular biology↗
bioRxiv2022

One Health Approach for the sampling of different bat species living in a sympatric colony

Bats are important contributors to the global ecosystems; at the same time, they are known to be a natural reservoir host for a number of human pathogenic viruses. These and many other unique features make them an interdisciplinary research object in the context of One Health, comprising zoology, ecology, virology, microbiology, molecular biology, immunology and public health issues. Performing field studies for bat research often aims to cover several of these topics and requires the combination of specific expertise in different fields. We carried out three individual field studies in Wavul Galge cave (Koslanda, Sri Lanka), where several bat species roost sympatrically. The main goals were to study the bat colony for ecological aspects and to sample bats for virological and molecular biological analyses. In the course of the field studies, we optimized the sampling procedure regarding safety aspects, a preferably low impact on the captured bats and an improved output of high-quality samples for further analysis. Different sampling methods and procedures were compared in order to establish a suitable strategy for frequent sampling and monitoring of these bats. In the present case study, we report on this process of optimizing our field work and provide suggestions for bat sampling methods that cause comparably less stress for the captured animals. We also report on constraints and obstacles encountered during the practical implementation and possible measures to overcome these. With these practical experiences, we hope to give support to other interdisciplinary research teams preparing for bat field work. Furthermore, we emphasize the need for the respectful treatment of the animals and minimized disturbance of their natural habitat when carrying out sustainable bat research.

zoology↗
bioRxiv2022

Comparative virome analysis of individual shedding routes of Miniopterus fuliginosus bats inhabiting the Wavul Galge Cave, Sri Lanka

Bats are described as the natural reservoir host for a wide range of viruses. Although an increasing number of bat-associated, potentially human pathogenic viruses were discovered in the past, the full picture of the bat viromes is not explored yet. In this study, the virome composition from Miniopterus fuliginosus bats inhabiting the Wavul Galge cave, Sri Lanka, was analyzed. To assess different possible shedding routes, oral swabs, feces and urine were collected and analyzed individually by using metagenomic NGS. The data obtained was further evaluated by using phylogenetic reconstructions. Two different alphacoronavirus strains were detected in feces and urine samples. Furthermore, a paramyxovirus was detected in urine samples. Sequences related to Picornaviridae, Iflaviridae, unclassified Riboviria and Astroviridae were identified in feces samples, and further sequences related to Astroviridae in urine samples. No further viruses were detected in oral swab samples. The comparative virome analysis in this study revealed a diversity in the virome composition between the collected sample types which also represent different potential shedding routes for the detected viruses. At the same time, several viruses were detected for the first time in bats in Sri Lanka. The detection of two different coronaviruses in the samples indicates the potential general persistence of this virus species in M. fuliginosus bats. Based on phylogenetics, the identified viruses are closer related to bat-associated viruses with comparably low human pathogenic potential. In further studies, the seasonal variation of the virome will be analyzed to identify possible shedding patterns for particular viruses.

molecular biology↗
bioRxiv2021

Molecular identification of bats from Wavulgalge cave, Wellawaya, Sri Lanka

This is the first report on the molecular identification and phylogeny of Rousettus leschenaultii, Rhinolophus rouxii, Hipposideros speoris, Hipposideros lankadiva, Miniopterus fuliginosus bat species in Sri Lanka, inferred from mitochondrially encoded cytochrome b gene sequences. Wellawaya Wavulgalge cave in Sri Lanka is one of the largest sympatric colonies found on the island, occupied by five species of bats. Recent research has indicated that bats show enormous cryptic genetic diversity. Moreover, even in the same species, acoustic properties of echolocation calls and morphological features such as fur colour could vary in different populations. Therefore, we have used molecular techniques for the accurate identification of five bat species recorded in one of the largest cave populations in Sri Lanka. Bats were caught using a hand net and saliva samples were collected non-invasively from each bat using a sterile oral swab. Nucleic acids were extracted from oral swab samples and mitochondrial DNA was amplified using primers targeting the mitochondrially encoded cytochrome b gene. This study identified the bat species recorded in the Wellawaya cave as Rousettus leschenaultii, Rhinolophus rouxii, Hipposideros speoris, Hipposideros lankadiva and Miniopterus fuliginosus. Our findings will contribute to future conservation and systematic studies of bats in Sri Lanka. This study will also provide the basis for a genetic database of Sri Lankan bats.

zoology↗
bioRxiv2021

Deep time course proteomics of SARS-CoV and SARS-CoV-2-infected human lung epithelial cells (Calu-3) reveals strong induction of interferon-stimulated gene (ISG) expression by SARS-CoV-2 in contrast to SARS-CoV

SARS-CoV and SARS-CoV-2 infections are characterized by remarkable differences, including contagiosity and case fatality rate. The underlying mechanisms are not well understood, illustrating major knowledge gaps of coronavirus biology. In this study, protein expression of SARS-CoV- and SARS-CoV-2-infected human lung epithelial cell line Calu-3 was analysed using data-independent acquisition mass spectrometry (DIA-MS). This resulted in the so far most comprehensive map of infection-related proteome-wide expression changes in human cells covering the quantification of 7478 proteins across 4 time points. Most notably, the activation of interferon type-I response was observed, which surprisingly is absent in other recent proteome studies, but is known to occur in SARS-CoV-2-infected patients. The data reveal that SARS-CoV-2 triggers interferon-stimulated gene (ISG) expression much stronger than SARS-CoV, which reflects the already described differences in interferon sensitivity. Potentially, this may be caused by the enhanced expression of viral M protein of SARS-CoV in comparison to SARS-CoV-2, which is a known inhibitor of type I interferon expression. This study expands the knowledge on the host response to SARS-CoV-2 infections on a global scale using an infection model, which seems to be well suited to analyse innate immunity.

systems biology↗
bioRxiv2020

Morphometry of SARS-CoV and SARS-CoV-2 particles in ultrathin sections of infected Vero cell cultures.

SARS-CoV-2 is the causative of the COVID-19 disease, which has spread pandemically around the globe within a few months. It is therefore necessary to collect fundamental information about the disease, its epidemiology and treatment, as well as about the virus itself. While the virus has been identified rapidly, detailed ultrastructural analysis of virus cell biology and architecture is still in its infancy. We therefore studied the virus morphology and morphometry of SARS-CoV-2 in comparison to SARS-CoV as it appears in Vero cell cultures by using conventional thin section electron microscopy and electron tomography. Both virus isolates, SARS-CoV Frankfurt 1 and SARS-CoV-2 Italy-INMI1, were virtually identical at the ultrastructural level and revealed a very similar particle size distribution with a median of about 100 nm without spikes. Maximal spike length of both viruses was 23 nm. The number of spikes per virus particle was about 30% higher in the SARS-CoV than in the SARS-CoV-2 isolate. This result complements a previous qualitative finding, which was related to a lower productivity of SARS-CoV-2 in cell culture in comparison to SARS-CoV.

microbiology↗
bioRxiv2020

Olfactory transmucosal SARS-CoV-2 invasion as port of Central Nervous System entry in COVID-19 patients

The newly identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a pandemic respiratory disease presenting with fever, cough, and often pneumonia. Moreover, thromboembolic events throughout the body including the central nervous system (CNS) have been described. Given first indication for viral RNA presence in the brain and cerebrospinal fluid and in light of neurological symptoms in a large majority of COVID-19 patients, SARS-CoV-2-penetrance of the CNS is likely. By precisely investigating and anatomically mapping oro- and pharyngeal regions and brains of 32 patients dying from COVID-19, we not only describe CNS infarction due to cerebral thromboembolism, but also demonstrate SARS-CoV-2 neurotropism. SARS-CoV-2 enters the nervous system via trespassing the neuro-mucosal interface in the olfactory mucosa by exploiting the close vicinity of olfactory mucosal and nervous tissue including delicate olfactory and sensitive nerve endings. Subsequently, SARS-CoV-2 follows defined neuroanatomical structures, penetrating defined neuroanatomical areas, including the primary respiratory and cardiovascular control center in the medulla oblongata.

neuroscience↗
bioRxiv2019

TaxIt: An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples

Untargeted accurate strain-level classification of a priori unidentified organisms using tandem mass spectrometry is a challenging task. Reference databases often lack taxonomic depth, limiting peptide assignments to the species level. However, the extension with detailed strain information increases runtime and decreases statistical power. In addition, larger databases contain a higher number of similar proteomes.\n\nWe present TaxIt, an iterative workflow to address the increasing search space required for MS/MS-based strain-level classification of samples with unknown taxonomic origin. TaxIt first applies reference sequence data for initial identification of species candidates, followed by automated acquisition of relevant strain sequences for low level classification. Furthermore, proteome similarities resulting in ambiguous taxonomic assignments are addressed with an abundance weighting strategy to improve candidate confidence.\n\nWe apply our iterative workflow on several samples of bacterial and viral origin. In comparison to non-iterative approaches using unique peptides or advanced abundance correction, TaxIt identifies microbial strains correctly in all examples presented (with one tie), thereby demonstrating the potential for untargeted and deeper taxonomic classification. TaxIt makes extensive use of public, unrestricted and continuously growing sequence resources such as the NCBI databases and is available under open-source license at https://gitlab.com/rki_bioinformatics.

bioinformatics↗
bioRxiv2018

PathoLive - Real time pathogen identification from metagenomic Illumina datasets

MotivationOver the past years, NGS has become a crucial workhorse for open-view pathogen diagnostics. Yet, long turnaround times result from using massively parallel high-throughput technologies as the analysis can only be performed after sequencing has finished. The interpretation of results can further be challenged by contaminations, clinically irrelevant sequences, and the sheer amount and complexity of the data. ResultsWe implemented PathoLive, a real-time diagnostics pipeline for the detection of pathogens from clinical samples hours before sequencing has finished. Based on real-time alignment with HiL-ive2, mappings are scored with respect to common contaminations, low-entropy areas, and sequences of widespread, non-pathogenic organisms. The results are visualized using an interactive taxonomic tree that provides an easily interpretable overview of the relevance of hits. For a human plasma sample that was spiked in vitro with six pathogenic viruses, all agents were clearly detected after only 40 of 200 sequencing cycles. For a real-world sample from Sudan the results correctly indicated the presence of Crimean-Congo hemorrhagic Fever Virus. In a second real-world dataset from the 2019 SARS-CoV-2 outbreak in Wuhan, we found the presence of a SARS Coronavirus as the most relevant hit without the novel virus reference genome being included in the database. For all samples, clinically irrelevant hits were correctly de-emphasized. Our approach is valuable to obtain fast and accurate NGS-based pathogen identifications and correctly prioritize and visualize them based on their clinical significance. AvailabilityPathoLive is open source and available on GitLab (https://gitlab.com/rkibioinformatics/PathoLive) and BioConda (conda install -c bioconda patholive). ContactBernhard.Renard@hpi.de, NitscheA@rki.de

bioinformatics↗
bioRxiv2017

Alzheimer related genes show accelerated evolution

Alzheimer's disease (AD) is a neurodegenerative disorder of unknown cause with complex genetic and environmental traits. Here, we show that gene structures of loci, that show AD-associated changes in their expression, evolve faster than the genome at large. This phylogenetic trait of AD suggests a critical pathogenetic role of recent adaptive evolution of human brain and might have far reaching consequences with respect to the appropriateness of model systems and the development of disease-modifying strategies.

evolutionary biology↗